Reverse Engineering Gene Regulatory Networks Related to Quorum Sensing in the Plant Pathogen Pectobacterium atrosepticum

  • Kuang Lin
  • Dirk Husmeier
  • Frank Dondelinger
  • Claus D. Mayer
  • Hui Liu
  • Leighton Prichard
  • George P. C. Salmond
  • Ian K. Toth
  • Paul R. J. Birch
Part of the Methods in Molecular Biology book series (MIMB, volume 673)


The objective of the project reported in the present chapter was the reverse engineering of gene regulatory networks related to quorum sensing in the plant pathogen Pectobacterium atrosepticum from micorarray gene expression profiles, obtained from the wild-type and eight knockout strains. To this end, we have applied various recent methods from multivariate statistics and machine learning: graphical Gaussian models, sparse Bayesian regression, LASSO (least absolute shrinkage and selection operator), Bayesian networks, and nested effects models. We have investigated the degree of similarity between the predictions obtained with the different approaches, and we have assessed the consistency of the reconstructed networks in terms of global topological network properties, based on the node degree distribution. The chapter concludes with a biological evaluation of the predicted network structures.

Key words

Pectobacterium atrosepticum Quorum sensing Transposon mutagenesis Microarrays Graphical Gaussian models Sparse Bayesian regression LASSO Bayesian networks Nested effects models Degree distribution Power law Gene ontologies 


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Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Kuang Lin
    • 1
  • Dirk Husmeier
    • 1
  • Frank Dondelinger
    • 2
  • Claus D. Mayer
    • 1
  • Hui Liu
    • 3
  • Leighton Prichard
    • 3
  • George P. C. Salmond
    • 4
  • Ian K. Toth
    • 3
  • Paul R. J. Birch
    • 3
  1. 1.Biomathematics and Statistics ScotlandEdinburgh & AberdeenUK
  2. 2.Biomathematics & Statistics Scotland and School of InformaticsUniversity of EdinburghEdinburghUK
  3. 3.Scottish Crop Research InstituteDundeeUK
  4. 4.Department of BiochemistryUniversity of CambridgeCambridgeUK

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